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- PDB-9xe6: Crimean-Congo hemorrhagic fever virus RNA polymerase containing a... -

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Basic information

Entry
Database: PDB / ID: 9xe6
TitleCrimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC
Components
  • RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3')
  • RNA (5'-R(*UP*UP*CP*CP*AP*AP*AP*AP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3')
  • RNA (5'-R(P*UP*CP*UP*C)-3')
  • RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-D(P*(CFZ))-3')
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN/RNA / RNA polymerase / VIRUS / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / Hydrolases; Acting on ester bonds / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / Hydrolases; Acting on ester bonds / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, nairovirus / : / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus ...RNA-directed RNA polymerase, nairovirus / : / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-2KH / : / RNA / RNA (> 10) / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsXue, L. / Gui, J. / Pan, H. / Chang, T. / Xiong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400116 to L.X, 82341085 to X.X China
CitationJournal: To Be Published
Title: Structural basis of RNA Synthesis and Inhibition by Small-Molecules in the Crimean-Congo Hemorrhagic Fever Virus Polymerase
Authors: Xue, L. / Gui, J. / Pan, H. / Chang, T. / Xiong, X.
History
DepositionOct 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA (5'-R(*UP*UP*CP*CP*AP*AP*AP*AP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3')
C: RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3')
D: RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-D(P*(CFZ))-3')
E: RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3')
F: RNA (5'-R(P*UP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,90712
Polymers471,1386
Non-polymers7686
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 448527.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on ester bonds, RNA-directed RNA polymerase

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RNA chain , 4 types, 5 molecules BCEDF

#2: RNA chain RNA (5'-R(*UP*UP*CP*CP*AP*AP*AP*AP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3')


Mass: 5966.608 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
#3: RNA chain RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3')


Mass: 6159.689 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
#4: RNA chain RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-D(P*(CFZ))-3')


Mass: 3146.939 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
#5: RNA chain RNA (5'-R(P*UP*CP*UP*C)-3')


Mass: 1177.738 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Crimean-Congo hemorrhagic fever virus strain IbAr10200

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Non-polymers , 3 types, 6 molecules

#6: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21769 / Symmetry type: POINT
RefinementHighest resolution: 3.09 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226993
ELECTRON MICROSCOPYf_angle_d0.5236624
ELECTRON MICROSCOPYf_dihedral_angle_d9.1494029
ELECTRON MICROSCOPYf_chiral_restr0.0394277
ELECTRON MICROSCOPYf_plane_restr0.0044445

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